Package bio.infer: Error Matching Taxa to ITIS Table

Hi Rich,

2007 is forever ago in software years: get.taxonomic() no longer has
an outputFile argument. If you can't figure out how to adapt the code
in the JSS article by reading the help files, then your best bet is
likely contacting the package maintainer to see if an updated version
of the article code might be available. Alternatively, you could try
the obsolete version of the package archived with the JSS article, but
that's not really recommended.

Sarah

  Following the example in Lester Yuan's 2007 paper in the Journal of
Statistical Software I've bumped into a fence and need help getting over it.

  My data is in the same data frame format as his bcnt.OR data set:

head(bioinfer)
          SVN              Taxon CountValue
1 WP220110711  Zaitzevia.parvula        484
2 WP220110711           Tvetenia        109
3 WP220110711        Tubificidae       1054
4 WP220110711            Sweltsa         11
5 WP220110711 Suwallia.pallidula         32
6 WP220110711     Stempellinella         11

and I implement the code on page 5 of this article:

library('bio.infer')

Loading required package: tcltk
Loading Tcl/Tk interface ... done

options(width = 60)
data('itis.ttable')
jercan <- get.taxonomic(bioinfer, itis.ttable, outputFile =
'sum.taxo.tbl.txt')

Error in get.taxonomic(bioinfer, itis.ttable, outputFile =
"sum.taxo.tbl.txt") :
  unused argument(s) (itis.ttable, outputFile = "sum.taxo.tbl.txt")

  I'd appreciate someone explaining the error message to me so I can fix it
and continue learning how to apply this package to my data.

Rich

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Sarah Goslee
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http://www.sarahgoslee.com
http://www.functionaldiversity.org

2007 is forever ago in software years: get.taxonomic() no longer has
an outputFile argument.

Sarah,

   Ah, so!

If you can't figure out how to adapt the code in the JSS article by
reading the help files,

I've read the .pdf that comes with the package but used the article to
learn the proper sequence of methods. I'll re-read the help files.

Thanks,

Rich

... get.taxonomic() no longer has an outputFile argument.

I've read the get.taxonomic() description in bio.infer.pdf and it works
... to a point. There are 3 taxa currently not in the ITIS database (a
freshwater worm, a midge, and one chironomid for which I can't track down
the genus). The first two are going through the validation process and will
be added to ITIS Real Soon Now. In the meantime, I don't know how to
proceed. So I've copied Lester Yuan on this message.

   I tell get.taxonomic() that I'm finished editing and it flashes a Tcl/Tk
window then ists the taxa not in the data base, but does not return the R
prompt:

jerall <- get.taxonomic(bioinfer)

The following taxa are not in ITIS:
EISENIELLA
RADOTANYPUS
ZIATZEVIA

   I've not found a key combination that lets me gracefully exit R (or emacs
for that matter); I can only kill the process. Nothing I've seen in the help
files appears relevant.

   Any suggestions?

Rich

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Hai Rich,

Have a look at our recently released taxize-package.
However we some some problems with the ITIS-API, too. (Maybe some server 
issues?)
See https://github.com/ropensci/taxize_/issues/72

However with taxize you can also query the NCBI taxonomy browser as 
alternative:

df <- read.table(header = TRUE, as.is = TRUE, text = 'SVN              
Taxon CountValue
1 WP220110711  Zaitzevia.parvula        484
2 WP220110711           Tvetenia        109
3 WP220110711        Tubificidae       1054
4 WP220110711            Sweltsa         11
5 WP220110711 Suwallia.pallidula         32
6 WP220110711     Stempellinella         11 ')
df$Taxon <- gsub("\\.", " ", df$Taxon)

require(taxize)

#query itis
classification(get_tsn(df$Taxon))
### This may fail sometimes. 'Connection reset by peer'
### we are working at it:
### see https://github.com/ropensci/taxize_/issues/72

# query ncbi taxonomy-browser instead
classification(get_uid(df$Taxon))


Hope this helps,

Eduard

On Mon, 10 Dec 2012, Sarah Goslee wrote:

... get.taxonomic() no longer has an outputFile argument.

  I've read the get.taxonomic() description in bio.infer.pdf and it works
... to a point. There are 3 taxa currently not in the ITIS database (a
freshwater worm, a midge, and one chironomid for which I can't track down
the genus). The first two are going through the validation process and 
will
be added to ITIS Real Soon Now. In the meantime, I don't know how to
proceed. So I've copied Lester Yuan on this message.

  I tell get.taxonomic() that I'm finished editing and it flashes a 
Tcl/Tk
window then ists the taxa not in the data base, but does not return the R
prompt:

jerall <- get.taxonomic(bioinfer)

The following taxa are not in ITIS:
EISENIELLA
RADOTANYPUS
ZIATZEVIA

  I've not found a key combination that lets me gracefully exit R (or 
emacs
for that matter); I can only kill the process. Nothing I've seen in 
the help
files appears relevant.

  Any suggestions?

Rich

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R-sig-ecology mailing list
R-sig-ecology at r-project.org
https://stat.ethz.ch/mailman/listinfo/r-sig-ecology